http://lod.bco-dmo.org/id/dataset/854887 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2021-06-29 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Sample and genetic accession information for RNA-seq data from whole Atlantic silverside (Menidia menidia) larvae from two populations and their F1 hybrids reared under different temperatures in 2017 2021-06-29 publication 2021-06-29 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2024-01-02 publication https://doi.org/10.26008/1912/bco-dmo.854887.1 Nina Overgaard Therkildsen Cornell University principalInvestigator Hannes Baumann University of Connecticut principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Therkildsen, N. O., Baumann, H. (2024) Sample and genetic accession information for RNA-seq data from whole Atlantic silverside (Menidia menidia) larvae from two populations and their F1 hybrids reared under different temperatures in 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-06-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.854887.1 [access date] Methods and Sampling: &lt;p&gt;&lt;strong&gt;Sampling and analytical procedures:&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;
Wild adults were caught at spawning time using seine nets at Jekyll Island, Georgia (GA; 3103N, 8126W) and Patchogue, New York (NY; 4045N, 7300W) in spring 2017. Individuals were transported live to the Rankin Seawater Facility at the University of Connecticuts Avery Point campus. A full reciprocal crossing design was set up by strip-spawning multiple males and females in batches onto mesh screens submerged in plastic dishes in seawater. We created reciprocal F1 crosses: NY♀ x NY♂ (NY), NY♀ x GA♂ (NYxGA), GA♀ x NY♂ (GAxNY), and GA♀ x GA♂ (GA). Fertilized eggs were kept in 20L rearing containers placed in large temperature-controlled water baths at constant salinity (30psu) and photoperiod (15L:9D). We split the fertilized eggs of each pure cross (NY and GA) into four batches, and hatched and reared two batches per cross at 20C and two batches at 26C. The hybrid crosses were each split into two batches, with one batch for each crossing direction incubated at either 20C or 26C. The two temperatures, 20C and 26C, were chosen to reflect the common rearing temperatures at both parental spawning locations (NY and GA), respectively. Individuals were reared to an approximate total length of 30mm, with the rearing durations differing between populations and temperature regimes. Most individuals from the GAxNY cross died at 26C and all at 20C and thus we could not include these crosses in present study. From the remaining crosses, we randomly selected 6-8 individuals for RNA-sequencing.&lt;/p&gt; &lt;p&gt;Total RNA was extracted from whole larvae (n=42) using the ZymoResearch Direct-zol Miniprep RNA plus kit. Whole larvae were homogenized in Trizol using a pestle prior to RNA extraction. During the extraction, an optional in-column DNAse I treatment step was performed to remove traces of genomic DNA from the sample, and samples were eluted in 50l of RNAse-free water and stored at -70C. RNA quantity was determined using the HS Assay kit for the Qubit 3.0 fluorometer (Life Technologies, Carlsbad, CA) and quality was assessed using a Fragment Analyzer (Agilent, Santa Clara, CA) at the Cornell University Biotechnology Resource Centre. RIN values ranged from 5.3 to 8.3, with an average RIN of 6.9. RNA-seq libraries were prepared at BGI Genomics using the stranded Illumina TruSeq mRNA sequencing kit with Poly-A selection.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Instruments:&lt;/strong&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;
Each library was sequenced to an average of 37.1M 2x150bp paired-end reads ( 0.194M s.d.) using an Illumina HiSeq 4000 sequencer at BGI Genomics.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Location:&amp;nbsp;&lt;/strong&gt;&lt;br /&gt; The larvae reared in the laboratory were F1 offspring of parents collected either in :&lt;/p&gt; &lt;p&gt;1) Jekyll Island, Georgia (31.02,-81.43), or&lt;br /&gt; 2) Patchogue, New York (40.75,-73.00)&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756316 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756316 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756751 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756751 completed Nina Overgaard Therkildsen Cornell University 607-255-2014 Department of Natural Resources 208 Fernow Hall Ithaca NY 14853 USA nt246@cornell.edu pointOfContact Hannes Baumann University of Connecticut 860-405-9297 Department of Marine Sciences 1080 Shennecossett Road Groton CT 06340-6048 USA hannes.baumann@uconn.edu pointOfContact asNeeded Dataset Version: 1 Unknown BioProject BioSample Sample_name SRA taxonomy_id taxonomy_name ecotype dev_stage sex tissue sample_type cross treatment Illumina HiSeq 4000 theme None, User defined NCBI BioProject accession NCBI BioSample accession sample identification NCBI SRA Sample accession (SRS) taxon_code taxon sample description water temperature at measurement depth featureType BCO-DMO Standard Parameters Automated DNA Sequencer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline https://befel.marinesciences.uconn.edu/2018/03/07/research-news-new-nsf-grant-to-study-silverside-genes/ Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline <p>NSF Abstract:</p> <p>Oceans are large, open habitats, and it was previously believed that their lack of obvious barriers to dispersal would result in extensive mixing, preventing organisms from adapting genetically to particular habitats. It has recently become clear, however, that many marine species are subdivided into multiple populations that have evolved to thrive best under contrasting local environmental conditions. Nevertheless, we still know very little about the genomic mechanisms that enable divergent adaptations in the face of ongoing intermixing. This project focuses on the Atlantic silverside (Menidia menidia), a small estuarine fish that exhibits a remarkable degree of local adaptation in growth rates and a suite of other traits tightly associated with a climatic gradient across latitudes. Decades of prior lab and field studies have made Atlantic silverside one of the marine species for which we have the best understanding of evolutionary tradeoffs among traits and drivers of selection causing adaptive divergence. Yet, the underlying genomic basis is so far completely unknown. The investigators will integrate whole genome sequencing data from wild fish sampled across the distribution range with breeding experiments in the laboratory to decipher these genomic underpinnings. This will provide one of the most comprehensive assessments of the genomic basis for local adaptation in the oceans to date, thereby generating insights that are urgently needed for better predictions about how species can respond to rapid environmental change. The project will provide interdisciplinary training for a postdoc as well as two graduate and several undergraduate students from underrepresented minorities. The findings will also be leveraged to develop engaging teaching and outreach materials (e.g. a video documentary and popular science articles) to promote a better understanding of ecology, evolution, and local adaptation among science students and the general public.</p> <p>The goal of the project is to characterize the genomic basis and architecture underlying local adaptation in M. menidia and examine how the adaptive divergence is shaped by varying levels of gene flow and maintained over ecological time scales. The project is organized into four interconnected components. Part 1 examines fine-scale spatial patterns of genomic differentiation along the adaptive cline to a) characterize the connectivity landscape, b) identify genomic regions under divergent selection, and c) deduce potential drivers and targets of selection by examining how allele frequencies vary in relation to environmental factors and biogeographic features. Part 2 maps key locally adapted traits to the genome to dissect their underlying genomic basis. Part 3 integrates patterns of variation in the wild (part 1) and the mapping of traits under controlled conditions (part 2) to a) examine how genomic architectures underlying local adaptation vary across gene flow regimes and b) elucidating the potential role of chromosomal rearrangements and other tight linkage among adaptive alleles in facilitating adaptation. Finally, part 4 examines dispersal - selection dynamics over seasonal time scales to a) infer how selection against migrants and their offspring maintains local adaptation despite homogenizing connectivity and b) validate candidate loci for local adaptation. Varying levels of gene flow across the species range create a natural experiment for testing general predictions about the genomic mechanisms that enable adaptive divergence in the face of gene flow. The findings will therefore have broad implications and will significantly advance our understanding of the role genomic architecture plays in modifying the gene flow - selection balance within coastal environments.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> GenomAdapt largerWorkCitation project eng; USA oceans -81.43 -73 31.02 40.75 2017-04-01 2017-08-01 Eastern coastline of North America 0 BCO-DMO catalogue of parameters from Sample and genetic accession information for RNA-seq data from whole Atlantic silverside (Menidia menidia) larvae from two populations and their F1 hybrids reared under different temperatures in 2017 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/870732.rdf Name: BioProject Units: unitless Description: <p>NCBI BioProject Identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/870733.rdf Name: BioSample Units: unitless Description: <p>NCBI BioSample Identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/870734.rdf Name: Sample_name Units: unitless Description: <p>Sample name</p> http://lod.bco-dmo.org/id/dataset-parameter/870735.rdf Name: SRA Units: unitless Description: <p>Sequence read archive sample accession</p> http://lod.bco-dmo.org/id/dataset-parameter/870736.rdf Name: taxonomy_id Units: unitless Description: <p>NCBI taxonomy identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/870737.rdf Name: taxonomy_name Units: unitless Description: <p>NCBI taxonomic name</p> http://lod.bco-dmo.org/id/dataset-parameter/870738.rdf Name: ecotype Units: unitless Description: <p>Population ancestry (pure F1 with both parents from Patchogue, New York, pure F1 with both parents from Jekyll Island, Georgia, and a hybrid F1 with one parent from each of the two populations)</p> http://lod.bco-dmo.org/id/dataset-parameter/870739.rdf Name: dev_stage Units: unitless Description: <p>Development stage</p> http://lod.bco-dmo.org/id/dataset-parameter/870740.rdf Name: sex Units: unitless Description: <p>Sex</p> http://lod.bco-dmo.org/id/dataset-parameter/870741.rdf Name: tissue Units: unitless Description: <p>Description of tissue sampled</p> http://lod.bco-dmo.org/id/dataset-parameter/870742.rdf Name: sample_type Units: unitless Description: <p>Sample type</p> http://lod.bco-dmo.org/id/dataset-parameter/870743.rdf Name: cross Units: unitless Description: <p>Information on the origin of parents (PANY = Patchogue, New York, JIGA = Jekyll Island, GA)</p> http://lod.bco-dmo.org/id/dataset-parameter/870744.rdf Name: treatment Units: degrees Celsius Description: <p>Treatment temperature</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 7303 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/392aa7ee-dee7-4658-a1ae-a2383c11945d/content download https://doi.org/10.26008/1912/bco-dmo.854887.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Sampling and analytical procedures:&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;
Wild adults were caught at spawning time using seine nets at Jekyll Island, Georgia (GA; 3103N, 8126W) and Patchogue, New York (NY; 4045N, 7300W) in spring 2017. Individuals were transported live to the Rankin Seawater Facility at the University of Connecticuts Avery Point campus. A full reciprocal crossing design was set up by strip-spawning multiple males and females in batches onto mesh screens submerged in plastic dishes in seawater. We created reciprocal F1 crosses: NY♀ x NY♂ (NY), NY♀ x GA♂ (NYxGA), GA♀ x NY♂ (GAxNY), and GA♀ x GA♂ (GA). Fertilized eggs were kept in 20L rearing containers placed in large temperature-controlled water baths at constant salinity (30psu) and photoperiod (15L:9D). We split the fertilized eggs of each pure cross (NY and GA) into four batches, and hatched and reared two batches per cross at 20C and two batches at 26C. The hybrid crosses were each split into two batches, with one batch for each crossing direction incubated at either 20C or 26C. The two temperatures, 20C and 26C, were chosen to reflect the common rearing temperatures at both parental spawning locations (NY and GA), respectively. Individuals were reared to an approximate total length of 30mm, with the rearing durations differing between populations and temperature regimes. Most individuals from the GAxNY cross died at 26C and all at 20C and thus we could not include these crosses in present study. From the remaining crosses, we randomly selected 6-8 individuals for RNA-sequencing.&lt;/p&gt; &lt;p&gt;Total RNA was extracted from whole larvae (n=42) using the ZymoResearch Direct-zol Miniprep RNA plus kit. Whole larvae were homogenized in Trizol using a pestle prior to RNA extraction. During the extraction, an optional in-column DNAse I treatment step was performed to remove traces of genomic DNA from the sample, and samples were eluted in 50l of RNAse-free water and stored at -70C. RNA quantity was determined using the HS Assay kit for the Qubit 3.0 fluorometer (Life Technologies, Carlsbad, CA) and quality was assessed using a Fragment Analyzer (Agilent, Santa Clara, CA) at the Cornell University Biotechnology Resource Centre. RIN values ranged from 5.3 to 8.3, with an average RIN of 6.9. RNA-seq libraries were prepared at BGI Genomics using the stranded Illumina TruSeq mRNA sequencing kit with Poly-A selection.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Instruments:&lt;/strong&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;
Each library was sequenced to an average of 37.1M 2x150bp paired-end reads ( 0.194M s.d.) using an Illumina HiSeq 4000 sequencer at BGI Genomics.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Location:&amp;nbsp;&lt;/strong&gt;&lt;br /&gt; The larvae reared in the laboratory were F1 offspring of parents collected either in :&lt;/p&gt; &lt;p&gt;1) Jekyll Island, Georgia (31.02,-81.43), or&lt;br /&gt; 2) Patchogue, New York (40.75,-73.00)&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;No processing.&lt;br /&gt; &lt;br /&gt; BCO-DMO data manager processing notes:&lt;br /&gt; * Extracted excerpts of sample information from NCBI in XML format.&amp;nbsp; Converted it to a tabular dataset (csv) and imported into BCO-DMO's data system to aid in dataset discovery and data reuse.&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina HiSeq 4000 Illumina HiSeq 4000 PI Supplied Instrument Name: Illumina HiSeq 4000 PI Supplied Instrument Description:Illumina HiSeq 4000 sequencer at BGI Genomics Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.